Prediction of Mucin type O-glycosylation sites, NetOglyc version 2.0:
NetOglyc is a neural network algorithm recognizing Mucin type
O-glycosylation sites in mammalian proteins.
The method have been updated with increased performance.
The method is available at:
http://www.cbs.dtu.dk/services/NetOGlyc/
both as a mail and www server.
The in vivo glycosylations sites used for making the method is
listed in O-GLYCBASE available at:
http://www.cbs.dtu.dk/databases/OGLYCBASE/
Abstract:
The specificities of the UDP-GalNAc:polypeptide
N-acetylgalactosaminyltransferase family which links the carbohydrate
GalNAc to the side chain of certain serine and threonine residues in
mucin type glycoproteins are presently unknown. The specificity seems
to be modulated by sequence context, secondary structure and surface
accessibility. The sequence context of glycosylated threonines was
found to differ from that of serine, and the sites were found to
cluster. Non-clustered sites had a sequence context different from
that of clustered sites. Charged residues were disfavoured at
position -1 and +3. A jury of artificial neural networks was trained
to recognize the sequence context and surface accessibility of 299
known and verified mucin type O-glycosylation sites extracted from
O-GLYCBASE. The cross-validated NetOglyc network system correctly
found 83 % of the glycosylated and 90 % of the non-glycosylated
serine and threonine residues in independent test sets, thus proving
more accurate than matrix statistics and vector projection methods.
--
Jan Hansen
Center for Biological Sequence Analysis
Department of Physical Chemistry
The Technical University of Denmark
Building 206
DK-2800 Lyngby
Denmark
Phone: +45 4525 2485
Fax: +45 4593 4808
E-mail: janhan at cbs.dtu.dk
WWW: http://www.cbs.dtu.dk/janhan/homepage.html